Hi,
I ran bowtie2 to align the fastq reads to align against a de novo assembled transcriptome. I ran the following command.
I obtained a sam file which I later converted it into a bam file and then sorted it out. When I open the bam file I found that for some transcripts has CIGAR value of less than 25M and has Read Sequence corresponding to CIGAR value. For an example, if the CIGAR for particular transcript is 12M and has the Read Sequence like ATGGCAGTGTTG. How could I interpret the information?
Kindly guide me
Regards
Deena
I ran bowtie2 to align the fastq reads to align against a de novo assembled transcriptome. I ran the following command.
Code:
bowtie2 -p 30 /path/to/bowti2_indexes -U Sample1.fastq -S Sample1.sam samtools view -F 4 -bS Sample1.sam -o Sample1.bam samtools sort Sample1.bam Sorted_Sample1
Kindly guide me
Regards
Deena
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